Update static docs

author: Johannes Ranke <jranke@uni-bremen.de> 2022-07-22 11:43:49 +0200
committer: Johannes Ranke <jranke@uni-bremen.de> 2022-07-22 11:43:49 +0200
commit: cff25a78e0e5a9d46db575b1ae3b02ace560aaf6 (patch)
tree: 9c4fb80c8725e4a82158c2955d26c805f3c65760
parent: 93256099d5c2536e8fab359d5afe58a361dc6139 (diff)
15 files changed, 651 insertions, 50 deletions
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 77cb0323..787fb371 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -38,6 +38,9 @@ reference:
       - "`[.mmkin`"
       - plot.mmkin
       - AIC.mmkin
+      - convergence
+      - illparms
+      - summary.mmkin
   - title: Mixed models
     desc: Create and work with nonlinear mixed effects models
     contents:
diff --git a/docs/404.html b/docs/404.html
index 7a6ede72..750f0ae7 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -32,7 +32,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span>
       </span>
     </div>
 
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 9cdfa9de..9a014b09 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span>
       </span>
     </div>
 
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 4e0cbba7..0b14fea2 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span>
       </span>
     </div>
 
@@ -105,7 +105,7 @@
       <h1 data-toc-skip>Benchmark timings for mkin</h1>
                         <h4 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 data-toc-skip class="date">Last change 1 July 2022 (rebuilt 2022-07-12)</h4>
+            <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-07-22)</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small>
       <div class="hidden name"><code>benchmarks.rmd</code></div>
@@ -116,20 +116,32 @@
     
 <p>Each system is characterized by the operating system type, the CPU type, the mkin version, and, as in June 2022 the current R version lead to worse performance, the R version. A compiler was available, so if no analytical solution was available, compiled ODE models are used.</p>
 <p>Every fit is only performed once, so the accuracy of the benchmarks is limited.</p>
+<p>The following wrapper function for <code>mmkin</code> is used because the way the error model is specified was changed in mkin version 0.9.49.1.</p>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/utils/packageDescription.html" class="external-link">packageVersion</a></span><span class="op">(</span><span class="st">"mkin"</span><span class="op">)</span> <span class="op">&gt;</span> <span class="st">"0.9.48.1"</span><span class="op">)</span> <span class="op">{</span></span>
+<span>  <span class="va">mmkin_bench</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, <span class="va">error_model</span> <span class="op">=</span> <span class="st">"const"</span><span class="op">)</span> <span class="op">{</span></span>
+<span>    <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, error_model <span class="op">=</span> <span class="va">error_model</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span>  <span class="op">}</span></span>
+<span><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span>
+<span>  <span class="va">mmkin_bench</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, <span class="va">error_model</span> <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">{</span></span>
+<span>    <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, reweight.method <span class="op">=</span> <span class="va">error_model</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span>  <span class="op">}</span></span>
+<span><span class="op">}</span></span></code></pre></div>
 <div class="section level2">
 <h2 id="test-cases">Test cases<a class="anchor" aria-label="anchor" href="#test-cases"></a>
 </h2>
 <p>Parent only:</p>
-<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">FOCUS_C</span> <span class="op">&lt;-</span> <span class="va">FOCUS_2006_C</span></span>
 <span><span class="va">FOCUS_D</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></span>
 <span><span class="va">parent_datasets</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">FOCUS_C</span>, <span class="va">FOCUS_D</span><span class="op">)</span></span>
 <span></span>
+<span></span>
 <span><span class="va">t1</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span><span class="op">)</span>, <span class="va">parent_datasets</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
 <span><span class="va">t2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span><span class="op">)</span>, <span class="va">parent_datasets</span>,</span>
 <span>    error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div>
 <p>One metabolite:</p>
-<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span>
 <span>  parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span>
 <span>  m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span>
@@ -145,7 +157,7 @@
 <span><span class="va">t5</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">FOCUS_D</span><span class="op">)</span>,</span>
 <span>    error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div>
 <p>Two metabolites, synthetic data:</p>
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">m_synth_SFO_lin</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span>
 <span>                           M1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span>
 <span>                           M2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span>
@@ -172,12 +184,6 @@
 <span>    error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span>
 <span><span class="va">t11</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">DFOP_par_c</span><span class="op">)</span>,</span>
 <span>    error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div>
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">mkin_benchmarks</span><span class="op">[</span><span class="va">system_string</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"t"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">11</span><span class="op">)</span><span class="op">]</span> <span class="op">&lt;-</span></span>
-<span>  <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">t1</span>, <span class="va">t2</span>, <span class="va">t3</span>, <span class="va">t4</span>, <span class="va">t5</span>, <span class="va">t6</span>, <span class="va">t7</span>, <span class="va">t8</span>, <span class="va">t9</span>, <span class="va">t10</span>, <span class="va">t11</span><span class="op">)</span></span>
-<span><span class="fu"><a href="https://rdrr.io/r/base/save.html" class="external-link">save</a></span><span class="op">(</span><span class="va">mkin_benchmarks</span>, file <span class="op">=</span> <span class="va">benchmark_path</span><span class="op">)</span></span>
-<span><span class="co"># Hide rownames from kable for results section</span></span>
-<span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">mkin_benchmarks</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="cn">NULL</span></span></code></pre></div>
 </div>
 <div class="section level2">
 <h2 id="results">Results<a class="anchor" aria-label="anchor" href="#results"></a>
@@ -322,8 +328,16 @@
 <td align="left">Ryzen 7 1700</td>
 <td align="left">4.2.1</td>
 <td align="left">1.1.1</td>
-<td align="right">1.809</td>
-<td align="right">3.468</td>
+<td align="right">1.770</td>
+<td align="right">3.377</td>
+</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 7 1700</td>
+<td align="left">4.2.1</td>
+<td align="left">1.1.2</td>
+<td align="right">1.962</td>
+<td align="right">3.606</td>
 </tr>
 </tbody>
 </table>
@@ -483,9 +497,18 @@
 <td align="left">Ryzen 7 1700</td>
 <td align="left">4.2.1</td>
 <td align="left">1.1.1</td>
-<td align="right">1.336</td>
-<td align="right">5.820</td>
-<td align="right">2.621</td>
+<td align="right">1.308</td>
+<td align="right">5.758</td>
+<td align="right">2.558</td>
+</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 7 1700</td>
+<td align="left">4.2.1</td>
+<td align="left">1.1.2</td>
+<td align="right">1.465</td>
+<td align="right">6.184</td>
+<td align="right">2.752</td>
 </tr>
 </tbody>
 </table>
@@ -693,12 +716,24 @@
 <td align="left">Ryzen 7 1700</td>
 <td align="left">4.2.1</td>
 <td align="left">1.1.1</td>
-<td align="right">0.707</td>
-<td align="right">1.148</td>
-<td align="right">1.339</td>
-<td align="right">2.812</td>
-<td align="right">1.752</td>
-<td align="right">2.594</td>
+<td align="right">0.696</td>
+<td align="right">1.124</td>
+<td align="right">1.321</td>
+<td align="right">2.786</td>
+<td align="right">1.744</td>
+<td align="right">2.566</td>
+</tr>
+<tr class="odd">
+<td align="left">Linux</td>
+<td align="left">Ryzen 7 1700</td>
+<td align="left">4.2.1</td>
+<td align="left">1.1.2</td>
+<td align="right">0.857</td>
+<td align="right">1.298</td>
+<td align="right">1.504</td>
+<td align="right">3.011</td>
+<td align="right">1.888</td>
+<td align="right">2.756</td>
 </tr>
 </tbody>
 </table>
diff --git a/docs/authors.html b/docs/authors.html
index afa0d11c..9daad578 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span>
       </span>
     </div>
 
@@ -109,13 +109,13 @@
 
     <p>Ranke J (2022).
 <em>mkin: Kinetic Evaluation of Chemical Degradation Data</em>.
-R package version 1.1.1, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. 
+R package version 1.1.2, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. 
 </p>
     <pre>@Manual{,
   title = {mkin: Kinetic Evaluation of Chemical Degradation Data},
   author = {Johannes Ranke},
   year = {2022},
-  note = {R package version 1.1.1},
+  note = {R package version 1.1.2},
   url = {https://pkgdown.jrwb.de/mkin/},
 }</pre>
 
diff --git a/docs/index.html b/docs/index.html
index 6e6a90fa..6118572b 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -44,7 +44,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span>
       </span>
     </div>
 
diff --git a/docs/news/index.html b/docs/news/index.html
index e7a7f571..d5c30552 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span>
       </span>
     </div>
 
@@ -82,6 +82,12 @@
     </div>
 
     <div class="section level2">
+<h2 class="page-header" data-toc-text="1.1.2" id="mkin-112">mkin 1.1.2<a class="anchor" aria-label="anchor" href="#mkin-112"></a></h2>
+<ul><li><p>‘R/convergence.R’: New generic to show convergence information with a method for ‘mmin’ objects.</p></li>
+<li><p>‘R/illparms.R’: New generic to show ill-defined parameters with methods for ‘mkinfit’ and ‘mmkin’ objects.</p></li>
+<li><p>‘R/summary.mmkin.R’: Summary method for mmkin objects.</p></li>
+</ul></div>
+    <div class="section level2">
 <h2 class="page-header" data-toc-text="1.1.1" id="mkin-111">mkin 1.1.1<a class="anchor" aria-label="anchor" href="#mkin-111"></a></h2>
 <ul><li><p>’R/{mkinmod,mkinpredict}.R: Store DLL information in mkinmod objects and use that information in mkinpredict to avoid a performance regression brought by a bugfix in R 4.2.x. Thanks to Tomas Kalibera for his analysis of the problem on the r-package-devel list and his suggestion on how to fix it.</p></li>
 <li><p>‘vignettes/FOCUS_L.rmd’: Remove an outdated note referring to a failure to calculate the covariance matrix for DFOP with the L2 dataset. Since 0.9.45.5 the covariance matrix is available</p></li>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 87309c06..9c5ace2f 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
   benchmarks: web_only/benchmarks.html
   compiled_models: web_only/compiled_models.html
   dimethenamid_2018: web_only/dimethenamid_2018.html
-last_built: 2022-07-12T10:10Z
+last_built: 2022-07-22T09:39Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/convergence.html b/docs/reference/convergence.html
new file mode 100644
index 00000000..3c7d5536
--- /dev/null
+++ b/docs/reference/convergence.html
@@ -0,0 +1,163 @@
+<!DOCTYPE html>
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+    </li>
+    <li>
+      <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
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+      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+    </li>
+    <li>
+      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+    </li>
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+      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
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+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Method to get convergence information</h1>
+    <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/convergence.R" class="external-link"><code>R/convergence.R</code></a></small>
+    <div class="hidden name"><code>convergence.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Method to get convergence information</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">convergence</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mmkin</span></span>
+<span><span class="fu">convergence</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for convergence.mmkin</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>object</dt>
+<dd><p>The object to investigate</p></dd>
+
+
+<dt>...</dt>
+<dd><p>For potential future extensions</p></dd>
+
+
+<dt>x</dt>
+<dd><p>The object to be printed</p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    
+
+<p>For <a href="mkinfit.html">mkinfit</a> objects, a character vector containing
+For <a href="mmkin.html">mmkin</a> objects, an object of class 'convergence.mmkin' with a
+suitable printing method.</p>
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">fits</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS A"</span> <span class="op">=</span> <span class="va">FOCUS_2006_A</span>,</span></span>
+<span class="r-in"><span>       <span class="st">"FOCUS B"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">convergence</span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>       dataset</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> model  FOCUS A FOCUS B</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   SFO  OK      OK     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   FOMC OK      OK     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> OK: No warnings</span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+</code></pre></div>
+    </div>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
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diff --git a/docs/reference/illparms.html b/docs/reference/illparms.html
new file mode 100644
index 00000000..037d7a8c
--- /dev/null
+++ b/docs/reference/illparms.html
@@ -0,0 +1,171 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Method to get the names of ill-defined parameters — illparms • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Method to get the names of ill-defined parameters — illparms"><meta property="og:description" content="Method to get the names of ill-defined parameters"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+<![endif]--></head><body data-spy="scroll" data-target="#toc">
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+    </li>
+    <li>
+      <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
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+      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+    </li>
+    <li>
+      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+    </li>
+  </ul></li>
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+  <a href="../news/index.html">News</a>
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+      </ul><ul class="nav navbar-nav navbar-right"><li>
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+</div><!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Method to get the names of ill-defined parameters</h1>
+    <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/illparms.R" class="external-link"><code>R/illparms.R</code></a></small>
+    <div class="hidden name"><code>illparms.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Method to get the names of ill-defined parameters</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mkinfit</span></span>
+<span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for mmkin</span></span>
+<span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for illparms.mmkin</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>object</dt>
+<dd><p>The object to investigate</p></dd>
+
+
+<dt>...</dt>
+<dd><p>For potential future extensions</p></dd>
+
+
+<dt>conf.level</dt>
+<dd><p>The confidence level for checking p values</p></dd>
+
+
+<dt>x</dt>
+<dd><p>The object to be printed</p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    
+
+<p>For <a href="mkinfit.html">mkinfit</a> objects, a character vector of parameter names
+For <a href="mmkin.html">mmkin</a> objects, an object of class 'illparms.mmkin' with a
+suitable printing method.</p>
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">illparms</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "parent_0" "alpha"    "beta"     "sigma"   </span>
+<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
+<span class="r-in"><span><span class="va">fits</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS A"</span> <span class="op">=</span> <span class="va">FOCUS_2006_A</span>,</span></span>
+<span class="r-in"><span>       <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">illparms</span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>       dataset</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> model  FOCUS A                      FOCUS C</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   SFO                                      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   FOMC parent_0, alpha, beta, sigma        </span>
+<span class="r-in"><span><span class="co"># }</span></span></span>
+</code></pre></div>
+    </div>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p>
+</div>
+
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+
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+
+
+  
+
+  </body></html>
+
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 63e3de8f..482edf08 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -17,7 +17,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.1</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span>
       </span>
     </div>
 
@@ -167,6 +167,18 @@ of an mmkin object</p></td>
           <p><code><a href="AIC.mmkin.html">AIC(<i>&lt;mmkin&gt;</i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i>&lt;mmkin&gt;</i>)</a></code> </p>
         </td>
         <td><p>Calculate the AIC for a column of an mmkin object</p></td>
+      </tr><tr><td>
+          <p><code><a href="convergence.html">convergence()</a></code> <code><a href="convergence.html">print(<i>&lt;convergence.mmkin&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Method to get convergence information</p></td>
+      </tr><tr><td>
+          <p><code><a href="illparms.html">illparms()</a></code> <code><a href="illparms.html">print(<i>&lt;illparms.mmkin&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Method to get the names of ill-defined parameters</p></td>
+      </tr><tr><td>
+          <p><code><a href="summary.mmkin.html">summary(<i>&lt;mmkin&gt;</i>)</a></code> <code><a href="summary.mmkin.html">print(<i>&lt;summary.mmkin&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Summary method for class "mmkin"</p></td>
       </tr></tbody><tbody><tr><th colspan="2">
           <h2 id="mixed-models">Mixed models <a href="#mixed-models" class="anchor" aria-hidden="true"></a></h2>
           <p class="section-desc"></p><p>Create and work with nonlinear mixed effects models</p>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 6d816366..17ecdfe4 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -21,7 +21,7 @@ values."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mat
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span>
       </span>
     </div>
 
@@ -95,70 +95,99 @@ values.</p>
     </div>
 
     <div id="ref-usage">
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mkinfit</span>
-<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, data <span class="op">=</span> <span class="cn">TRUE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, alpha <span class="op">=</span> <span class="fl">0.05</span>, <span class="va">...</span><span class="op">)</span>
-
-<span class="co"># S3 method for summary.mkinfit</span>
-<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, data <span class="op">=</span> <span class="cn">TRUE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, alpha <span class="op">=</span> <span class="fl">0.05</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for summary.mkinfit</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div id="arguments">
     <h2>Arguments</h2>
     <dl><dt>object</dt>
 <dd><p>an object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd>
+
+
 <dt>data</dt>
 <dd><p>logical, indicating whether the data should be included in the
 summary.</p></dd>
+
+
 <dt>distimes</dt>
 <dd><p>logical, indicating whether DT50 and DT90 values should be
 included.</p></dd>
+
+
 <dt>alpha</dt>
 <dd><p>error level for confidence interval estimation from t
 distribution</p></dd>
+
+
 <dt>...</dt>
 <dd><p>optional arguments passed to methods like <code>print</code>.</p></dd>
+
+
 <dt>x</dt>
 <dd><p>an object of class <code>summary.mkinfit</code>.</p></dd>
+
+
 <dt>digits</dt>
 <dd><p>Number of digits to use for printing</p></dd>
+
 </dl></div>
     <div id="value">
     <h2>Value</h2>
-    <p>The summary function returns a list with components, among others</p>
+    
+
+<p>The summary function returns a list with components, among others</p>
 <dl><dt>version, Rversion</dt>
 <dd><p>The mkin and R versions used</p></dd>
+
 <dt>date.fit, date.summary</dt>
 <dd><p>The dates where the fit and the summary were
 produced</p></dd>
+
 <dt>diffs</dt>
 <dd><p>The differential equations used in the model</p></dd>
+
 <dt>use_of_ff</dt>
 <dd><p>Was maximum or minimum use made of formation fractions</p></dd>
+
 <dt>bpar</dt>
 <dd><p>Optimised and backtransformed
 parameters</p></dd>
+
 <dt>data</dt>
 <dd><p>The data (see Description above).</p></dd>
+
 <dt>start</dt>
 <dd><p>The starting values and bounds, if applicable, for optimised
 parameters.</p></dd>
+
 <dt>fixed</dt>
 <dd><p>The values of fixed parameters.</p></dd>
+
 <dt>errmin </dt>
 <dd><p>The chi2 error levels for
 each observed variable.</p></dd>
+
 <dt>bparms.ode</dt>
 <dd><p>All backtransformed ODE
 parameters, for use as starting parameters for related models.</p></dd>
+
 <dt>errparms</dt>
 <dd><p>Error model parameters.</p></dd>
+
 <dt>ff</dt>
 <dd><p>The estimated formation fractions derived from the fitted
 model.</p></dd>
+
 <dt>distimes</dt>
 <dd><p>The DT50 and DT90 values for each observed variable.</p></dd>
+
 <dt>SFORB</dt>
 <dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd>
+
 </dl><p>The print method is called for its side effect, i.e. printing the summary.</p>
     </div>
     <div id="references">
@@ -176,19 +205,19 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
 
     <div id="ref-examples">
     <h2>Examples</h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span>
-<span class="r-in">  <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for fitting:    1.1.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:       4.2.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Wed May 18 20:42:00 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Wed May 18 20:42:00 2022 </span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for fitting:    1.1.2 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:       4.2.1 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Fri Jul 22 11:39:29 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Fri Jul 22 11:39:29 2022 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - k_parent * parent</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 131 model solutions performed in 0.027 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted using 131 model solutions performed in 0.028 s</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Error model: Constant variance </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -220,9 +249,9 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Parameter correlation:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>               parent_0 log_k_parent     sigma</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0     1.000e+00    5.428e-01 1.648e-07</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_parent 5.428e-01    1.000e+00 2.514e-07</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> sigma        1.648e-07    2.514e-07 1.000e+00</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0     1.000e+00    5.428e-01 1.642e-07</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_parent 5.428e-01    1.000e+00 2.507e-07</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> sigma        1.642e-07    2.507e-07 1.000e+00</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Backtransformed parameters:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Confidence intervals for internally transformed parameters are asymmetric.</span>
@@ -252,7 +281,7 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
 <span class="r-out co"><span class="r-pr">#&gt;</span>    62   parent     5.98    10.862  -4.8818</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    90   parent     1.54     3.831  -2.2911</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   118   parent     0.39     1.351  -0.9613</span>
-<span class="r-in"></span>
+<span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
   </div>
@@ -267,7 +296,7 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
 </div>
 
 <div class="pkgdown">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p>
 </div>
 
       </footer></div>
diff --git a/docs/reference/summary.mmkin.html b/docs/reference/summary.mmkin.html
new file mode 100644
index 00000000..dfbd766e
--- /dev/null
+++ b/docs/reference/summary.mmkin.html
@@ -0,0 +1,173 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Summary method for class "mmkin" — summary.mmkin • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Summary method for class " mmkin summary.mmkin><meta property="og:description" content="Shows convergence information on the mkinfit objects contained in the object
+and gives an overview of ill-defined parameters calculated by illparms."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
+
+    <div class="container template-reference-topic">
+      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">mkin</a>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span>
+      </span>
+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav"><li>
+  <a href="../reference/index.html">Functions and data</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu"><li>
+      <a href="../articles/mkin.html">Introduction to mkin</a>
+    </li>
+    <li>
+      <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+    </li>
+    <li>
+      <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+    </li>
+    <li>
+      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+    </li>
+  </ul></li>
+<li>
+  <a href="../news/index.html">News</a>
+</li>
+      </ul><ul class="nav navbar-nav navbar-right"><li>
+  <a href="https://github.com/jranke/mkin/" class="external-link">
+    <span class="fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+
+      </header><div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Summary method for class "mmkin"</h1>
+    <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary.mmkin.R" class="external-link"><code>R/summary.mmkin.R</code></a></small>
+    <div class="hidden name"><code>summary.mmkin.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Shows convergence information on the <a href="mkinfit.html">mkinfit</a> objects contained in the object
+and gives an overview of ill-defined parameters calculated by <a href="illparms.html">illparms</a>.</p>
+    </div>
+
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, <span class="va">...</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S3 method for summary.mmkin</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>object</dt>
+<dd><p>an object of class <a href="mmkin.html">mmkin</a></p></dd>
+
+
+<dt>conf.level</dt>
+<dd><p>confidence level for testing parameters</p></dd>
+
+
+<dt>...</dt>
+<dd><p>optional arguments passed to methods like <code>print</code>.</p></dd>
+
+
+<dt>x</dt>
+<dd><p>an object of class <code>summary.mmkin</code>.</p></dd>
+
+
+<dt>digits</dt>
+<dd><p>number of digits to use for printing</p></dd>
+
+</dl></div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">fits</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS A"</span> <span class="op">=</span> <span class="va">FOCUS_2006_A</span>,</span></span>
+<span class="r-in"><span>       <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Error model: Constant variance </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 0.607 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Convergence:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>       dataset</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> model  FOCUS A FOCUS C</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   SFO  OK      OK     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   FOMC OK      OK     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> OK: No warnings</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Ill-defined parameters:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>       dataset</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> model  FOCUS A                      FOCUS C</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   SFO                                      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   FOMC parent_0, alpha, beta, sigma        </span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+    </div>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p>
+</div>
+
+      </footer></div>
+
+  
+
+
+  
+
+  </body></html>
+
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index f39832fb..ba8f37e6 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -103,6 +103,9 @@
     <loc>https://pkgdown.jrwb.de/mkin/reference/confint.mkinfit.html</loc>
   </url>
   <url>
+    <loc>https://pkgdown.jrwb.de/mkin/reference/convergence.html</loc>
+  </url>
+  <url>
     <loc>https://pkgdown.jrwb.de/mkin/reference/create_deg_func.html</loc>
   </url>
   <url>
@@ -124,6 +127,9 @@
     <loc>https://pkgdown.jrwb.de/mkin/reference/get_deg_func.html</loc>
   </url>
   <url>
+    <loc>https://pkgdown.jrwb.de/mkin/reference/illparms.html</loc>
+  </url>
+  <url>
     <loc>https://pkgdown.jrwb.de/mkin/reference/ilr.html</loc>
   </url>
   <url>
@@ -262,6 +268,9 @@
     <loc>https://pkgdown.jrwb.de/mkin/reference/summary.mkinfit.html</loc>
   </url>
   <url>
+    <loc>https://pkgdown.jrwb.de/mkin/reference/summary.mmkin.html</loc>
+  </url>
+  <url>
     <loc>https://pkgdown.jrwb.de/mkin/reference/summary.nlme.mmkin.html</loc>
   </url>
   <url>
diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda
index d507131a..14ae6346 100644
--- a/vignettes/web_only/mkin_benchmarks.rda
+++ b/vignettes/web_only/mkin_benchmarks.rda
author	Johannes Ranke <jranke@uni-bremen.de>	2022-07-22 11:43:49 +0200
committer	Johannes Ranke <jranke@uni-bremen.de>	2022-07-22 11:43:49 +0200
commit	cff25a78e0e5a9d46db575b1ae3b02ace560aaf6 (patch)
tree	9c4fb80c8725e4a82158c2955d26c805f3c65760
parent	93256099d5c2536e8fab359d5afe58a361dc6139 (diff)